Ring-shaped workpieces are commonly utilized in high-precision measuring instruments, and their thermal deformation affects the instruments’ measuring accuracy. A novel method for establishing the thermal deformation model of ring-shaped workpieces is proposed in this article. The mechanism of thermal deformation caused by shape boundaries is investigated using the principle of molecular dynamics. A mathematical model between deformation degree and height, diameter ratio, or temperature is created using a large-scale atomic/molecular massively parallel simulator. The established model is verified by measuring the thermal deformation of ring-shaped workpieces. The model is used to optimize laser collimation systems, and stability experiments for laser collimation systems in different sizes are performed. The stability of optimized systems can be improved by 50%, 50%, and 48% with temperature increases of 10 °C, 20 °C, and 30 °C, respectively. The experimental results indicate the obtained model can be utilized to improve the stability of instruments.